Code for animal id marking

ABSTRACT

An animal identification code is described comprising two numbers, one of which is encoded into a human-readable marking and the other of which is encoded into a machine-readable marking, where the two numbers and the two encodings are different. The combination of the two numbers, plus additional information not marked on a first animal, such as time of read, is looked up a first table to determine conditional validity and from there to a second table to determine a valid and unique animal ID associated with the animal, a primary key. The animal may be a rodent in a vivarium and the markings may be tattooed on the animal tail. The second marking may be a vine code with a spine where the spine is aligned with the animal tail. The first number may be unique within a first animal population such as an animal study. The combination of the first and second marking may be reused on a second animal wherein the lifetimes of the first and second animal do not overlap. The primary key is unique among all animals in a third population, dead or alive.

This application is a continuation of and claims priority to applicationSer. No. 15/252,699 filed on Aug. 31, 2016.

No new matter has been added.

FIELD OF THE INVENTION

The invention relates to management of animals in a vivarium for bothhusbandry and study purposes. More specifically it relates to uniquelyidentifying animals in the vivarium. Yet more specifically, it isdirected to marking, such as by tattooing, both machine-readable andhuman-readable identification markings on an animal, such as tattooing acombination of alphanumerics and a barcode on the tail of a rodent.

BACKGROUND

Vivaria house a number of animals, typically test animals, such as mice,in a number of cages, often a large number. The test animals arefrequently used to test drugs, genetics, animal strains, husbandryexperiments, methods of treatment, procedures, diagnostics, and thelike. We refer to all such uses of a vivarium as a study.

The animals in a vivarium must be observed, either manually by humans orby automated means, such as by the use of video cameras and imageprocessing. Observations and comparisons of animals are the basis ofstudy results.

There are a large number of animal characteristics, attributes, orbehavior that may be of interest in a study. We refer to all suchobservable aspects of animals as “behaviors,” including blood, saliva,feces, urine, breath, and fur attributes. Observations of behaviors maybe manual or automated and may be invasive or non-invasive. They mayoccur in the animal's home cage; or in a separate observation or testcage or apparatus; or via pathology or other chemical, biological oranalytical analysis. Observations and results may use statistics oraggregated behaviors.

For observing all such behaviors, it is critical that the observedbehaviors be reliably, easily, and quickly linked to one particularanimal. It is also necessary that marking the animals be consistent,fast, reliable and low cost. Prior art uses a variety of animalidentification systems, including one animal per cage, ear notches, eartags, foot and toe pad tattooing, embedded RFID, attached RFID, bodytattoos, and tail tattoos. Some prior art uses human-readable markings,such as ear notches or ID numbers tattooed on a tail. Some prior artuses machine-readable markings, such as RFIDs, ear-tag barcodes, andtail barcodes.

In an ideal world, each animal might receive a globally unique ID thatis never re-used. However, that requires a large code space, which inreturn requires complex markings. Small animal tails are a poor choicesubstrate for placing printed codes. Complex codes either cannot bemarked at all, or do not read reliably. In prior art practice, markingsare often in a very small code space and other systems are used touniquely identify an animal. One such prior art method is a marking thatis unique only within a single cage. For example, colored ear tags maybe used, with only five colors available. Alternatively, ear notches maybe used providing a code space size of less than 100. Another prior artmethod uses unique markings within a single study. Animals in one studyare generally kept well apart from animals in another study; thus,unique marking within one study may be sufficient.

All such prior art has significant weaknesses. For machine-readablemarkings weaknesses include:

-   -   risk of confusing one animal with another, for example, if an        animal is moved to a wrong cage    -   not human-readable    -   slow reading    -   requires specialized equipment    -   expensive equipment and expensive to read    -   computer required to read and map animal ID    -   may have single-vendor lock-in    -   two hands often required to use equipment    -   accuracy and reliability may not be computable or traceable    -   slow and expensive to mark animals    -   limited through rate for marking new animals    -   animals may have to be a minimum age to mark    -   may work only in-cage or may work only out-of-cage    -   either applying marks or reading marks may not be sterile    -   animal may have to anesthetized to be marked.

For human-readable markings weaknesses include:

-   -   risk of confusing one animal with another, for example, if an        animal is moved to a wrong cage        -   * often not machine-readable    -   may not be readable in the dark—the animals' natural activity        period    -   reading may be unreliable    -   typically has a small code space    -   requires manual data entry to link animal ID to stored data    -   likely not suitable for machine marking    -   high labor cost for marking    -   accuracy and reliability may not be computable or traceable    -   limited through rate for marking new animals    -   slow through rate for marking new animals.

Embodiments of this invention overcome many of the weaknesses of priorart.

SUMMARY OF THE INVENTION

A problem to be solved is how to place a reliably readable code ormarking on an animal using a small code space and yet maintain uniqueanimal identification within a required set or subset of animals.

The prior art uses either simple, large markings in a small space forreliability, such as five colors of animal ear tags; or uses manysmaller markings taking up a large space, such a barcode, to achieveuniqueness within a larger population of animals. In the first priorart, uniqueness is achieved only over a very small population, suchanimals in a single cage. In the second prior art, both convenience,such as human readability, and reliability, such as by using tinymarkings, is lost.

This invention achieves the above goals of reliability, readability, anduniqueness by using two markings, one human-readable and onemachine-readable, and also by associated the pair of markings with atime window corresponding to the life of an animal. The pair of markingsmay then be re-used on a different animal with a non-overlappinglifetime. In addition, the human-readable markings may be selected suchthat they are unique within a smaller population, such as a singlestudy. The first marking is associated with a first number, and thesecond marking with a second number. Marking and number may or may notbe the same. A combination of the first number, the second number and atime window is mapped into a primary key that is unique for all animalsever placed in the vivarium.

Thus, there are three exemplary scenarios for using such an invention:

First, a human technician observing or handling animals within a studyneed only observe, memorize briefly, and then record a short number ofcharacters (the human-readable marking) for each animal. Alternatively,the technician may be prompted with a short number and then needs onlyconfirm that the right animal is selected or observed. The short numberassures reliable human reading and reliable short-term memorization.

Second, machine vision is used to read both the human-readable markingsand the machine-readable markings on all live animals in the vivarium.This pair of markings is unique for all live animals in the vivarium. Inthis way, no live animal can be mistaken for any other live animal.

Third, machine vision is used to read both the human-readable markingand the machine-readable marking on all animals in the vivarium in abrief time period, such as one day or one minute. This pair of markings,plus the read time, is then mapped to a fully unique primary key foreach animal. In this way, no animal can be mistaken for any otheranimal, dead or alive, within the time the system in place in one ormore vivaria.

Two mapping tables may be used. The first mapping table uses acombination of the first number and the second number, and a time, as anindex. A valid entry in the first table maps to a second table with aprimary key, which is a unique identifier for all animals, dead oralive. The second table provides additional information about theanimal. The first table may be used as a preliminary read validitycheck. The second table provides a final read validity check.

A human-readable marking may be a few digits. A machine-readable markingmay be a vine code or a modified vine code with a spine.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a rodent tail with a combined marking tattooed.

FIG. 2 shows prior art.

FIG. 3 shows an exemplary vine code with a spine.

FIG. 4 shows a combined human-readable and machine-readable markingcombination.

FIG. 5A shows an exemplary human-readable marking.

FIG. 5B shows an exemplary human-readable symbol set.

FIG. 5C shows an exemplary set of capital letters missing from ahuman-readable symbol set.

FIG. 6 shows a combination code table with time windows and a primarykey table.

FIG. 7 shows multiple probability sets.

FIG. 8 shows an automated or manual device for tattooing rodent tails.

FIGS. 9A and 9B illustrate one exemplary embodiment.

FIG. 10 shows a graphical view of limitations of a first embodiment.

DETAILED DESCRIPTION OF THE INVENTION

Prior art barcodes use one code or marking to identify an object. Mostoften, the barcode is essentially a font or encodes a number, such as adecimal or a binary number. The characters or number encoded is then theobject identifier. Within some context or scope, that identifier ishopefully unique. Prior art barcodes generally assume reliable printingor marking, with some codes allowing for read errors by means of checkdigits, parity, CRC, checksums, or forward error correction. Prior artalso assumes a uniform or consistent surface on which the barcode isprinted or placed.

Animal ID marking, particularly for animals in a vivarium, including butnot limited to rodents, have several unique requirements.

First, marking may not be reliable. In fact, if marking is accomplishedby tattooing then marking errors may occur more frequently than readingerrors. Thus, it is desirable to have a code that allows for correctionof mismarked code symbols.

Second, not only is there limited space on which to place animal IDs,particularly on a rodent tail, but also the idealized codes space islarge: being ideally globally unique codes for all animals for all time.These two conditions are in direct conflict, as a large code spacerequires a physically larger mark, for a given resolution and desiredreliability.

Third, accuracy of reading animal ID is critical in a vivarium. A singlemisread ID may compromise or invalidate a study. Thus, not only shouldreads be valid, but also error rates should be computable so as toprovide a credible confidence level for both ID reads and study results.

Fourth, there is typically a requirement for an animal code to be bothhuman-readable and machine-readable. While such a requirements exists inmany other barcode applications and is solved by simply replicated thedata once as a machine-readable barcode and again as human-readabletext, the space for marking animal ID is extremely limited and thus thisspace-inefficient duplication of the same information is not practical.

Fifth, the human-readable marking should be one that is quickly andeasily memorized by a human technician or handler, who may well haveboth hands full and thus not able to readily copy an animal code ontopaper or a keyboard. This requirement indicates a short code should beused, using symbology that is easy for people to memorize quickly andreliably. However, a short code is in direct conflict with desire tosupport a large code space.

Sixth, a rodent tail is long and thin. Therefore, at least for themachine-readable marking, an output symbology that uses short-height orshort-width symbols is desirable. While prior art barcodes, as parallellines, support short symbols, prior art barcodes are inadequate for thisapplication, as explained herein.

Seventh, a common method of marking rodent tails is by use of tattoo.Tattoo heads mark points or lines at effectively a fixed width. Priorart barcodes typically use variable line width a part of the code. Suchvariable width lines are not compatible with standard tattoo heads.

Eight, rodent tails are live and change length as the animal grows. Inaddition, the tails both grow unevenly. In addition, live animal tailcurvature typically changes rapidly. Prior art barcodes typically usevariable line spacing as part of the code. Such variable width linespacing is not compatible with realities of changing tail length,curvature and space due to growth and live animal activity.

Ninth, controlling a tattooing head, with respect to a rodent tail, isdifficult for both manual and automated operation. Therefore, thesymbology used must mitigate these practical limitations. In particular,short line segments and diagonal lines are less reliably formed thanperpendicular lines and line segments in one of a small number of fixedlengths.

Tenth, because live rodent tails changes shape rapidly, it is desirableto have a symbology that inherently provides local curvatureinformation. Although humans are excellent at reading text on curves,automated systems are not. Prior art barcodes do not support dynamicallycurving substrates.

Eleven, the width (diameter) of a rodent tale tapers from somewhat widenear the animal to narrow near the tip of the tale. Because of the verylimited area in which to mark a rodent tale, it is desirable to have acode that takes advantage of the “tapered aspect ratio” of the rodenttail. Prior art barcodes assume a consistent, rectangular aspect ratioof the available substrate area. In addition, because much of the tailis narrow, in practice, only a portion of the tail nearest the animalbody is suitable for marking readable codes.

Twelfth, it is critical in vivarium applications that reading animal IDsis both highly reliable and that reliability (error rate) is computable.Some prior art uses “check digits” to catch errors. However, checkdigits are very inefficient. For example, a single check digit, assuminguniform and random errors, catches only 90% of errors, leaving a 10%uncaught error rate. To get a 0.1% (one out of one thousand) error rateit is necessary to use three check digits. If the animal code is threedigits to start with, then the use of check digits doubles the necessaryanimal area. Some codes use error correction, such as parity orReed-Solomon codes. Such error correction is most efficient for longerdata blocks. The short data blocks of the animal ID do not supportefficient error correction. For example, a 20-bit animal code wouldtypically require another 14 bits for Reed-Solomon bits. Therefore,forward error correction is not an effective means to detect read errorsin this application.

Thirteenth, many prior art methods of marking animals, includingrodents, requires anesthetizing the animal prior to marking. Suchanesthetizing is slow, expensive, stresses the animals, and requiresspecialized equipment. Placement of RFIDs or marking areas other thanthe tail typically requires anesthetizing. Some prior art markingmethods, such as notching ears or punching in ear tags is painful forthe animal and stresses the animal.

Fourteenth, it is desirable to minimize the cost of marking each animal;minimize the need for specialized equipment; minimize reliance on asingle vendor for equipment or supplies; minimize the need forspecialized training of the humans doing the marking; and provide forhigh throughput of marking new animals. Prior art methods generally aretime consuming to mark, making them costly; or use specialized equipmentor vendor-lock-in equipment or supplies (including ink cartridges orpre-manufactured ear tags); or are difficult to perform, requiringspecialize training, which also limits the number of personnel availablefor marking and also limits throughput. Specialized equipment may alsolimit throughput.

Fifteenth, because it is desirable to keep code size at a minimumsubject to all other requirements, it is desirable to be able to“re-use” animal codes, even if full animal IDs are not reused. Prior artbarcodes, being effectively fonts, do not permit effective index tables(such as in a database) that may be updated to permit re-use of animalcodes. Note that we here distinguish between the “animal code” or“animal marking,” which is marked on the animal, and the “animal ID,”which is the ID associated with the animal for data recording and isunique within the scope of that animal ID. Such a unique animal ID maybe called a primary key. A first table may be used to convert the animalcode to the animal primary key, where the index into the first table isthe animal code and a field at that line of the table is the primarykey, as well as optional other data about either the animal code or theanimal, or other related data. For this use, the animal code may also becalled a “token,” and the table called a “token table.” A second table,indexed by the primary key, typically provides much more informationabout the animal. Code read validity may be determined first by thefirst table and then finally by the second table.

Sixteenth, it is desirable to integrate the animal management, includingmarking and reading, with computer data about the animals, studies andvivarium. Prior art barcodes, being simple font representations ofpredetermined text strings or numbers, have no inherent integration. Inaddition, such integration is typically always required in a vivarium.Prior art codes do not take advantage of such integration to implementthe desired features of animal making and animal codes, as describedherein, or to mitigate weaknesses, as described herein. Therefore, it isdesirable to take advantage of computer integration, computer databases,and computerized number selection, as part of the animal marking andanimal ID system.

Seventeenth, prior art animal marking codes and methods often use smallor extremely small code spaces. The minimum effective code space ismarking uniquely each animal in one cage. For this purpose, sometimescolors are used. Five colors limit the number of animals in a cage tofive. In addition, colors are typically not easily machine-readable. Inparticular, they cannot be read in infrared light, meaning they cannotbe read during the normal nocturnal activity period of mice. Ear notchesmight have a code space of about 20, which is adequate for one cage.However, ear notches hurt the animals and are also subject to a largehuman error rate as some notches may not be seen, or the ears may becomedamaged, or a human reader may mix up the two ears. Ear notches are verydifficult to machine-read.

Eighteenth, it is desirable to be able to have a human-readable markingavailable to a human if both of the human's hands are full. This meansthat the need to hold a barcode reader to read a mouse ID isundesirable. In addition, the need for a barcode reader for every mouseinteraction is time-consuming and requires a large amount of expensive,specialized equipment.

Nineteenth, barcoded ear tags are undesirable because (i) they areexpensive; (ii) they have single-vendor lock-in; (iii) they may not beavailable with the codes desired; (iv) they are not directlyhuman-readable; (v) they require both operator hands to use (one to holdthe mouse and one to hold the reader); (vi) they typically require theoperation to be online to a computer in order to read the mouse ID.Paper and pencil may not be substituted, even temporarily; (vii) theymay not be tolerated by the mouse; (viii) they may be chewed by othermice; (ix) relatively small amounts of detritus, such as food or blood,will make the code unreadable; (x) the animal will not do anyself-cleaning of the ear tag. (However, they will self-clean their owntails.)

Twentieth, and of particular importance, animal IDs in a vivarium aretypically needed in two separate scopes: the first scope is within onestudy and the second scope includes the entire vivarium. A scope of asingle cage is poor for several reasons. One is that the cage numbermust be used in order to make the mouse ID unique within a study. Thisintroduces several sources of errors and also makes cage swapping, ormoving mice between cages both cumbersome and error prone, as theindexing system must be properly and timely updated. It also means thatmice from more than one cage cannot be intermixed. If they areaccidentally intermixed, all those mice must be removed from the studyimmediately. Therefore, it is strongly desirable that a mouse ID beunique within a single study. Study sizes may vary from about five miceup to many hundreds. Therefore, a codes space of at least five hundredis typically necessary for animal ID within a study. Animals fromdifferent studies are rarely intermixed. Often the cages for one studyare physically segregated from cages used in another study. Therefore,often knowing only the animal ID unique for one study is adequate for alarge percent of animal handling and animal ID activities. It isadvantageous to have the animal code unique to a study to behuman-readable, as this meets many of the above numbered requirements ordesires.

Twenty-first, it is desirable to be able to use both a machine, such asshown in FIG. 8, and manual marking, to mark codes on animal tails.Typically, barcodes are too complex to mark by hand.

With regards to the scope being the entire vivarium, it is necessary atvarious times and locations to assure than animals from one study areunquestionably part of that study, and that study animals are notintermixed, and that the absolute identity of every animal within avivarium, or within a group of vivaria which might ever move or shareanimals, be known without risk of error, or with an extremely small andcomputable error. Thus, animals need to be permanently marked in someway with a code space equal to the maximum possible number of animals ina vivarium, and in addition provide some means of validating valid readsof this animal code. Such a code space is in the range of 100,000 to onemillion, and might even be larger in some applications.

We use the term “animal code” or “marked code” for one or more markedcodes that are placed on the animal. These consist of symbols from acode output symbol set. The number of symbols used in the marked codedetermines the size of the code space.

We use the term “animal ID” as a unique ID for an animal within a studyor within another scope. There may be a mapping from one or more themarked codes to an animal ID.

Embodiments of this invention include marking codes on an animal using acombination comprising both a machine-readable portion and ahuman-readable portion.

Embodiments of this invention place codes via tattooing on a rodenttail.

Embodiments of this invention include a human-readable portion that isalso machine-readable.

The machine-readable portion, in one embodiment, is a vine code. Aparticular code is described below. A variation on prior art codesincludes the use of a “spine” marking perpendicular to the normal codelines.

The human-readable portion is, in one embodiment, one or morealphanumeric characters from a reduced set of alphanumeric characterswhere the reduced set has the attributes of (i) symbols that are easilymistaken for a different symbol are deleted from the symbol set; (ii)all symbols may be drawn and easily read using only orthogonal, linearline segments.

In one embodiment, the human-readable portion comprises the digits 0-9,which may be marked with a combination of straight lines oftenreferenced to “seven-segment” digits.

In one embodiment, the code space size of the human-readable portion isappropriate to provide a unique code for each animal in a study,assuming the largest reasonable study size.

In one embodiment, the human-readable portion of the animal code is anindex that maps to a sparse index table, wherein the index tableprovides a unique animal ID for animals within one study. Indexes may bere-usable in other parallel or future studies.

In one embodiment, the machine-readable portion of the code provides aunique study ID. In one embodiment the machine-readable portion of thecode is an index that maps to a sparse study ID index table.

In one embodiment, error detection of the human-readable portion of theanimal code is provided by using a sparse animal ID index table, whereinan animal code that does not map to a valid animal ID is detected as aread error in the animal code.

In one embodiment, error detection of the machine-readable portion ofthe animal code is provided by using a sparse study ID index table,wherein a machine-readable portion that does not map to a valid study IDis detected as a read error for the machine-readable portion of theanimal code.

In one embodiment the machine-readable portion of the animal code mustmap to a valid study ID and, in addition, the human-readable portion ofthe animal code must map to a valid animal ID table in the animal IDindex table for the valid study ID. In this way the mapping of both themachine-readable portion and the human-readable portion must properlymap within sparse tables for a read to be valid.

In one embodiment the human-readable marking is also machine-readable.

In one embodiment the number used for the human-readable marking and thenumber used for the machine-readable marking are combined into a numberlooked up in a single animal ID table. The animal ID table provides keyinformation about the animal, such as its study, cage number, and muchmore information. The animal ID table likely provides links of some typeto additional data. Entries in the animal ID table may be the targetlinks of links from other tables or sources. Additional data may be usedfor lookups, such as time, a cage, and the like.

In some embodiments either the numbers used for the human-readablemarkings, or the numbers used for the machine-readable markings, orboth, are selected by a method that minimizes potential read errors bymaximizing the multi-dimensional “distance” between used markings.

One such type of distance measurement is Hamming distance, althoughmethods of determining distance may be used.

Note that there is no specific requirement, in some embodiments, for thehuman-readable portion to be specifically associated with an animal IDwithin one study, and there is no specific requirement that themachine-readable portion be specifically associated with a study ID. Forexample, in one embodiment, the combined machine-readable and thehuman-readable portions may be viewed as a single animal code into alarger, sparse table that provides both a study ID and an animal ID, forthat animal code. The human-readable portion might also be unique withina study, or other scope, such that the human-readable portion issufficient to identify an animal within a vivarium application.Combining the human-readable portion with the machine-readable portionprovides a far larger potential code space, making the correspondingindex table much sparser, increasing the change that a misread of theentire code will be caught.

Animal codes portions, for either portion of the animal code, may beassigned randomly, pseudo-randomly, or by the use of other assignmentalgorithms. A key goal of any such assignment algorithm is that likelyor random misreads have a high, or equal, probability of being caught.Such mapping algorithms are well known in the art. Ideally, animalcodes, animal IDs, study codes and study IDs are distributed in anapparent arbitrary or random throughout the available corresponding codespaces.

One embodiment uses a vine code for the machine-readable portion. Byvine code we mean a code using a sequence of parallel lines segments ofvarying length, and optionally a variable offset from a perpendicularread axis. This class of codes is well known including such standardcodes as PostBar, POSTNET and RM4SCC. Machine-readable codes includebarcodes, 2D (or matrix) codes, OCR, and many others. Traditionalbarcodes generally vary either the width of the bar or the spacingbetween the bars (or both) for encoding. 2D (or matrix) codes typicallyhave a 2D grid or arrangement of cells wherein each cell is on or off,such as black or white. In the case of vine codes, neither the width ofthe bar nor the spacing between bars changes. Barcode terminology variesgreatly. Therefore it is necessary to construe terms associated withbarcodes in the context in which they are used.

There are a large number of proposed, previously used, and currentlyused machine-readable codes. Most of these were created to meet theneeds of a particular application, such as postal codes on envelopes orfruit codes on oval fruit stickers. Embodiments of this inventioninclude codes optimized for the application of this invention:machine-readable markings on rodent tails.

One embodiment comprises a vine code with a spine. The spine is a linealong the read axis; that is, perpendicular to the parallel linesegments that make up leaves. In prior art bar codes are normally thoughof as horizontal. However, in this application for convenience we thinkof a vine code and thus its spines as vertical, with orthogonal bars, orleaves, as horizontal with leaf elements identified as left or right.PostBar, POSTNET and RM4SCC do not use an explicit spine. These codeswere designed for use on envelopes, for example, that do notsignificantly distort. Prior art vine codes use a variety of encodings,often have special segments within a printed code that are encodeddifferently, may or may not use “start” and “stop” codes, may or may notuse parity, and may or may not use error-correction elements. Prior artvine codes are not configured to support printing or reading on curves.Prior art vine codes do not have an ability to mark out or delete aleaf, or to add a replacement leaf.

However, rodent tails are very flexible and reading a code on a rodenttail must deal with the tail being straight or significantly curved. Inaddition, the tail may be rotated so that the “center” of the parallelline segments, or the reference axis or reference line, is hard todetermine. Thus, for the particular application of this invention, avisible spine permits video analytics (or other machine vision) to trackthe tail curvature, rotation and position, and thereby reliably read theleaf locations, positions, and length reliably.

For convenience we refer to each line segment or bar as a “leaf.” Theremay or may not be a starting or an ending leaf. In one embodiment a leafthat is longer than an otherwise valid leaf length is specificallyreserved to mark that leaf as “deleted.” In some embodiments areplacement leaf may be provided either following the deleted leaf, orat the end of the vine code, or in another location.

In one embodiment, each leaf (if not deleted) encodes two bits. The leafsegments may be left, right, full width, or missing (for a null leaf).In addition, an extra long leaf may denote a “deleted” leaf.

Note that it is desirable, and used in some embodiments, to use a hashor another “randomization” one-to-one transformation to createpseudo-random bit streams or high-entropy bits streams within the vinecode so that there is an unlikely chance of a long string of “zeroes”which might be encoded as a null leaf. Another method of preventing thissituation is simply not use any such animal codes. Since they areindexes, there is no loss of arbitrary animal IDs or study IDS, up tothe codes space size available. Yet another method is the use of severalwell know line codes or run length limited (RLL) code maps, such as5b/6b, 8b/10b, RLL (2,7) or RLL (1,7) that assure a maximum run-lengthof either consecutive zeros or ones. Alternatively, a convolution codemay be used.

For the human-readable portion, it is desirable to have code symbolsthat can be easily and reliably marked, such as by tattooing. Also, thesymbols should be able to be quickly and reliably read by humans. In oneembodiment, all such symbols are created from seven connected linesegments, where each segment is present or absent, the segments are allparallel or perpendicular to each other, and the seven segments, if allpresent form the digit, “8.” Such a format is well known in the art as a“seven-segment display.” Such displays do a good job of presentinghuman-readable digits 0 through 9. However, displaying the completeroman capital letter alphabet (A through Z) in such a display requiresmapping some letters to unconventional forms. We refer generally to thisencoding per character as “seven segment.”

Therefore, for one embodiment, a reduced alphanumeric symbol set isused. This set is created by starting with a 36-symbol set of ten digitsplus 26 letters, then deleting all symbols that either (i) look likeanother symbol in the set, or (ii) cannot be readily mapped to an easilyrecognizable capital letter in the “seven segment” format. One suchcharacter set uses the characters shown in FIG. 5B. Alternativecharacter sets created by the same or similar rules, for the samepurpose, are specifically claimed under the Rule of Equivalents. Thisincludes, for example, the addition of symbols or lower-case letters.This includes, for example, deletion of d, n, r, or T.

A simple robot, or machine, is described below that is suitable forautomatic marking of the described codes on a rodent tail.

Novelty

A novelty of embodiments is to use both a human-readable marking portionand a machine-readable marking portion. Such two portions may bemarkings from a human-readable encoding and a machine-readable encoding.In one embodiment these two portions use different encodings. In oneembodiment, these animal code portions are marked on an animal's tail,such as a rodent tail. In one embodiment the animal code portions aretattooed. The tattooing may be manual or automated.

FIG. 1 shows an exemplary human-readable marking 11 and an exemplarymachine-readable marking 12 on a rodent tail 13. 10 is the body end ofthe tail; 13 is the tip of the tail. 14 shows a partial rodent body.

In some embodiments the human-readable marking is also machine-readable.

In some embodiments, the human-readable marking portion is unique withina first population, such as a single study. In some embodiments, thecombination of the human-readable marking and the machine-readablemarking is unique for all live animals in a vivarium. In someembodiments a combination of the human-readable marking, themachine-readable marking, and a read time is unique for all suitablymarked animals in the vivarium, independent if the animal is dead oralive.

In some embodiments, the selection of human-readable markings, or theselection of machine-readable markings, or both, are selected on thebasis of maximizing Hamming distance of sub-symbols (i.e., Hammingsymbols) within the marked codes.

Not all embodiments have the above limitations.

Continuing with FIG. 1, we see both a human-readable marking 11 and amachine-readable marking 12 marked on a rodent tail 13. The rodent maybe a mouse. The method of marking may be tattooing.

Continuing with FIG. 1, the machine-readable marking portion 12 may be avine code, with or without a spine. It may be a barcode known in theart. The spine is aligned with the tail such that the code is easy toread with machine vision, as the spine clearly demarks the location andcurvature of the tail, and also provides a reference point fordetermining if the bars, (or “leaves”) in the code are left, right,full-width or null. A rodent tail may not only curve dynamically withrodent activity, but also rotate around the tail axis. The tail may alsocurve upward. Thus, a code spine is valuable to determine all suchdistortions from an ideal, flat, rectangular, fixed substrate for thecode marking. In addition, the tail may be partially covered withdetritus, such as bedding or other material. A continuous spine makes iffar easier to determine reliably if a portion of the machine-readablemarking is so obscured. In addition, a printed spine may be used todetermine the start and end of the printed code; that is, the locationsof the first and last leaf. This is particularly important when thefirst or last leaf is a null leaf.

Prior art required white or black cage bottoms to machine-read a tailbarcode. Prior art required cages to be free of bedding, as that mightobscure a portion of the code, causing a misread. Use of a vine codewith a spine eliminates these requirements as the dark markings on alight tail provide sufficient contrast, and use of a spine does notrequire that the edges of the tail be identifiable.

In some embodiments, either the human-readable or the machine-readablemarking portions 11 and 12 respectively is an identifier within a knownscope. In some embodiments such a scope might be all animals in a studyor in a set of cages, or require a particular procedure or observation.In some embodiments the scope is all the live animals in a vivarium. Insome embodiments the scope is all the animals in a group of vivaria.

In some embodiments the combination of the human-readable and themachine-readable marking portions is an animal identifier within a knownscope, such as all live animals.

The combination of the human-readable and the machine-readable markingportions may be a third animal code, where the third animal code must belooked up in a third animal code mapping table comprises an entry(field) comprising to a primary key that uniquely identifies an animal.

The code space of the machine-readable marking portion may be no morethan 10,000; 100,000; 1,000,000; 10,000,000; or 100,000,000. The codespace of the machine-readable marking portion may be no more than 12bits, 14 bits, 16 bits, 18 bits, 20 bits, 22 bits 24 bits, 26 bits, or28 bits. The code space of the machine-readable marking portion may inthe range of 12-14 bits, 12-16 bits, 14-18 bits, 16-20 bits, 18-22 bits,20-24 bits, or 22-28 bits, 14-20 bits, or 16-28 bits. Themachine-readable marking portion may or may not comprise check bits,parity bits, checksums, CRC, and forward error correction.

The animal in FIG. 1 on which both a human-readable marking and amachine-readable marking have been placed may have no additional placedmarkings. Indeed, the ability to identify animal with no additionalmarkings are the benefits of key embodiments.

Turning now to FIG. 2 we see exemplary prior art. There is no visiblespine. An ascender bar or leaf is shown 20. A descender leaf 21 isshown. A full-height leaf 22 is shown. A minimal leaf 23 is shown. Themachine-readable marking in this Figure is made human-readable byreplicating the data in the code as text 24. Note that this code has nonull leaves and no printed spine.

FIG. 2 shows a prior art vine code. This is an example of one of anumber of postal code symbologies. Prior art vine code symbologies donot have a marked spine. Prior art vine code symbologies have noprovision for marking a bar as deleted and have no provision for addinga replacement bar for a deleted bar. Prior art vine code symbologies usepre-determined encodings and do not use a dynamic lookup table to mapfrom a printed code to an actual identifier, such as a primary key orother animal ID. That is, prior art codes are merely fixed definitionfonts, not an index.

Turning now to FIG. 3, we see an exemplary vine code of one embodiment.30 is a full-width leaf. 31 is a right leaf. 32 is a left leaf. Location33 shows a null leaf. 34 shows a fixed-width gap between leaves. Nullleaves, such as 33, are detected by noticing that the gap betweenadjacent leaves is twice the fixed-width gap 34 plus the thickness ofone line segment. A null leaf is also detected when the start or end ofthe spine extends past the last visible leaf. Note that the prior artcode in FIG. 2 does not have null leaves.

In some embodiments, each leaf of the vine code may encode two bitseach. In some embodiments, two bits may be encoded as one of: (i) aright leaf 31; (ii) a left leaf 32; (iii) a full-width leaf 30; or (iv)a null leaf 33. In some embodiments a leaf that is longer than afull-width leaf may be used to indicate a deleted leaf position or amarking error. In this Figure, line width is not part of the coding. Inthis Figure, the spacing 34 between leaves is fixed: line thickness isnot part of the coding. In one embodiment, line spacing 34 is not fixedand is not part of the coding either. An advantage over prior art isthat by ignoring line thickness in the coding, the significant real-timeand growth-based dynamics of a rodent tail do not distort the markedcode so as to reduce the reliability of reads or cause misreads. Even ifany such misread rate is low, the misread rate is not accuratelycomputable. In addition, both line thickness and line spacing aredifficult to control when tattooing, whether the tattooing is donemanually or by a robot.

An exemplary vine code, such as shown in FIG. 3, may encode 8-14 bits,12-16 bits, 14-18 bits, 16-20 bits, 18-22 bits, 20-24 bits, or 22-28bits, 14-20 bits, or 8-28 bits. The vine code may or may not comprisecheck bits, parity bits, checksums, CRC, and forward error correction.Specific vine codes to mark may be selected such that a Hammingdistance, where the “Hamming symbols” are each short line segment in aleaf, is maximized amongst all used codes, or amongst a subset of usedcodes. All leaves in the shown code have two short line segments. A fullwidth leaf has two marked short line segment regions. A null leaf hastwo unmarked short line segments. Left and right leaves have one markedand one unmarked short line segment.

Turing now to FIG. 4, we see an exemplary combination of both ahuman-readable marking portion 41 and a machine-readable marking portion42. Here the human-readable marking 41 is of the number 348. Thecharacters are printed in the common “seven-segment” format. However,other fonts or character formats may be used. The machine-readablemarking 42 is a four-leave vine code where each leaf is one of fourpossible leaf symbols. This code marking has a spine, which is verticalin the Figure. The top-most leaf is full-width. The second leaf is null.The third leave is right. The fourth leaf is left. Thus, 42 in thisFigure shows all four leaf symbols. This code encodes 2*4=8 bits, or 256possible input values. The three-digit numeric marking codes 1000possible input values, from 0 to 999. Thus, the combination of thehuman-readable marking and the machine-readable marking encodes256*1000=256,000 possible input values.

Turning now to FIGS. 5A and 5B, we see an exemplary symbology for thecharacters in a human-readable marking. All characters may be formed bya non-empty subset of seven straight-line segments, arranged in awell-known “seven-segment” formation. The use of this formation isuniquely advantageous for tattooing rodent tails because each linesegment may be formed by motion along only one axis. The motion may bemanual or automated. Either the rodent (or the platform on which therodent rests) may be moved, or the tattooing apparatus may be moved. Inone embodiment, motion along the axis of the tail is implemented bysupporting a tattooing head on a linear track, which in turn may besupported by a gantry or other support structure. In one embodiment, theother axis may be implemented by rotating the tail around the tail axis.For manual tattooing, such rotation may be via one or more finger(s)gently placed on the tail. For automatic tattooing, a motorized rubberfinger or fingers may be used, effectively operating similar to manualoperation. Tattooing movement along only one axis at a time is fareasier for human operators, which is a unique problem, and for whichthis code symbology is a novel solution. See also FIG. 8.

FIG. 5A shows an exemplary coded mark, here the three characters “348,”using the exemplary symbol set shown in FIG. 5B. Note that all symbolsshown in FIG. 5B may be formed from a subset of the seven-segment linesegments. Note that all symbols shown in FIG. 5B are readilyidentifiable without confusion with other symbols, and also readilymemorized in codes. The marking shown in FIG. 5A may also use onlydecimal digits as its input set.

The symbol set for the human-readable marking may comprise analphanumeric character set comprising digits and Roman letters such asshown in FIG. 5B. The human-readable marking may comprise only digits,as shown in FIG. 5A. The human-readable marking may comprise analphanumeric character set comprising digits and limited Roman letterssuch that the remaining Roman letters in the character set are easilyrecognizable and clearly distinguishable from digits or other Romancharacters. The human-readable marking portion may be one character, twocharacters, three characters, four characters, or five characters, orthe range of 1-2, 1-3, 1-4, 2-3, 2-4, or 3-4 characters. One suchreduced character set is shown in FIG. 5B. Here, the letters “D” and “N”are represented more closely to their traditional lower case appearance:“d” and “n” respectively. The letters T and Y appear asymmetric in thecode; however, they are still easily identifiable by people. Within thecontext of our claims, we explicitly claim all similar reduced charactersets, similarly reduced for readability in a seven-segment format, underthe Rule of Equivalents.

FIG. 5C shows Roman characters not used in the exemplary symbol set dueto their similarity to other digits or characters.

Another embodiment uses the seven line-segment basis expanded to ninesegments by the addition of two, three, or four diagonal segments in theupper and lower rectangles formed within the digit “8.” The addition ofthese diagonal segments permits the full 36-character alphanumericcharacter set to be distinctly marked.

Numeric only and alpha only symbol sets are expressly claimed asalternative embodiments to an alphanumeric symbols set.

Turning now to FIG. 6, we see exemplary elements of importantembodiments. Table 70 is a “marking table” that may be used to look up agiven marking on an animal. Column 71 contains values of ahuman-readable marking. Column 72 contains values of a machine-readablemarking. Column 73 contains a time window. Column 74 contains a link toa primary key, or a value of a primary key. If a particularhuman-readable marking value, machine-readable marking value, and timeis in the table, such as shown in row 76 and 77, then the link in column74 will point to a valid primary key. If a particular human-readablemarking value, machine-readable marking value, and time is not in thetable, there may be no matching table row, or the field in column 74 maybe null, or there is indeed an entry for a primary key but the record,in table 80, shows that the primary key is not valid for this readcontext. Note that typically a lookup in table 70 has a “read time”associated with it. For the lookup to have a valid row in the table, theread time must be within the time window in the field in column 73.Roughly, each valid row in table 70, such as rows 76 and 77, correspondsto one animal. Note that the same human-readable marking and samemachine-readable marking may be marked on two different animals, atdifferent times. For example, rows 76 and 77 show this. The time windowvalues of TIME 1 and TIME 2 do not overlap. Thus, for any given readtime, at most only one read row would be valid. Typically, time windowsare associated with a lifetime or expected lifetime of an animal.

Table 80 is the primary key table. Column 81 holds the field for theprimary key. The primary key is unique for all animals participating inthis system. For example, it may be unique for all animals ever in avivarium or in a group of vivaria. 82 shows schematically other fieldsin each record. Typically, there may be 30 to 50 fields, comprisinginformation such as species, source, birthdate, cage number, one or morestudies, treatments, outcomes, death date, links to other information,and much more information about a single animal per primary key. Table80 shows primary keys for two animals, 38745 and 99471. These animalswould not be alive at the same time because we see from rows 76 and 77in table 70 that they have the same code markings.

Note that FIG. 6 is illustrative only, showing tables 70 and 80 as flattables. In practice, many other implementations are possible, such asthe use of relational databases, objects, dictionaries, arrays, othertable types, and the like. Arrows 75 and 78 show the relationshipbetween the records 76 and 77 in table 70 and the records associatedwith primary keys 38745 and 99471 in table 80, respectively.

FIG. 7 shows one method of reading marked codes. Here a code symbolbeing read has one of ten values, shown as the digits 1 through 9 andzero. Table 90 shows the results of image processing for one frame. Theheight of each of the ten bars represents a relative or absoluteprobability that the mark is actually the symbol of that column. Tables91 show similar tables where each table is from a different frame,however for the same location on the same animal tail. Table 92 showsthe sum or average of all of the tables in 90 and 91. There may be 2 to100 such individual tables. As can be seen in bar 95, the symbol has themost likelihood of being a “5.” It has a lower likelihood of being thesymbol, “0,” shown as the height of bar 96. The distance 95 shows therelative or absolute probability difference that the symbol is a “5”versus a “0.”

A method similar to the one shown in FIG. 7 may be used to readmachine-readable markings such as a vine code. In this case, there wouldbe four values in each table, rather than ten. For either thehuman-readable marking where each symbol is a digit or themachine-readable marking where each symbol is a leaf, this process isrepeated for each symbol. For example, if the marked code comprisesthree digits, the process shown in the Figure would be repeated threetimes. If the marked code comprises four leaves, the process shown inthe Figure would be repeated four times. The most probably symbol foreach position is then looked up in table 70 from FIG. 6. If there is novalid entry, then a next most likely symbol may be substituted, such asshown by bar 96 in FIG. 7. In this way, the first most probably set ofsymbols that is valid is chosen.

FIG. 8 shows an automated or manual marking machine. Here, 50 is a mouseon a work surface 51. Rollers 55 are used to roll the tail back andforth. Such motion may be used to mark line segments perpendicular tothe tail, 57. 56 and 57 show the mouse tail. 56 is nearer the tip of thetail; this region is not suitable for marking. 57 shows a tail portioncloser to the body of the mouse; this region is suitable for marking. Amarking head, such as a tattooing head is shown as 53. The head issupported on a frame, 52. The head is capable of two directions ofmotion as shown by the arrows: axially along the tail and vertically toraise or lower a tattoo tip, 54.

FIGS. 9A and 9B provide a helpful illustration of one embodiment. InFIG. 9A we see that a first number passes through a first encoding togenerate a first marking. A second number passes through a secondencoding to generate a second marking. The first and second markings areboth marked on a first animal; let's call this first animal, “Bob.” Afirst primary key is associated uniquely with Bob; we can call thisprimary key, “Bob's primary key.” Bob's primary key is unique for allanimals in a first population, such as all animals ever in a vivarium. Afirst time window is associated with Bob's primary key. A combination ofthe first number, the second number, and a time may be used to index to,that is, locate uniquely, Bob's primary key. The number may be viewed asan input to the encoding and the marking may be viewed as an output. Theencoding may be the use of a font.

FIG. 9B shows a second animal, which we can call, “Alice.” The samefirst and second numbers pass through the same first and secondencodings to generate the same first and second markings as for Bob inFIG. 9A. These same first and second markings are marked on Alice. Alicealso has a primary key. Since her primary key is unique it is inherentlydifferent than Bob's primary key. A second time window is associatedAlice's primary key. A combination of the first number, the secondnumber, and a time may be used to index to, that is, locate uniquely,Alice's primary key. Clearly the time used for the Bob's primary keylookup is different than the time used for Alice's primary key lookup.The number may be viewed as an input to the encoding and the marking maybe viewed as an output.

For FIGS. 9A and 9B the lifetimes of Bob and Alice do not overlap. Thus,in practice, although they both have the same markings, any reading ofthose markings can be used to distinguish Alice from Bob by the time ofthe reading.

In one embodiment both the first and second animals are free of anyadditional markings.

In some embodiments, animals in a second animal population, smaller thanthe first population, such as animals in one study, have unique firstmarkings.

Turning now to FIG. 10, we see a graphical, schematic representation oflimitations of original system claim 1 as filed for this application.The reference designators, 1 a through 1 t, align, generally, with theclaim limitations as originally identified (a) through (t). No newmatter has been added. Claim 1 in this application contains the samelimitations as claims 1, 9 and 10 in the originally filed parentapplication.

The overall FIG. 1 a, shows limitations as applied to a vivarium, orelements or method steps associated with the vivarium. Two animals areshown: a first animal labeled Animal #1 and a second animal labeledAnimal #2. Shown are exemplary animals: mice. Shown is a time window T1associated with the first animal and a time window T2 associated withthe second animal. Timelines T1 and T1 may be lifetimes or expectedlifetimes of the associated animals, or they may be a period of timewhen the animal is used in a study, or another associated time window. 1b is a, “first number.” Here, an exemplary number 348 is shown; however,no limitation on a “number” is implied by this example. 1 c is a “firstencoding,” indicated by an arrow from the first exemplary number 348 toa, “first encoding” of the first number, 1 f. 1 d is a, “second number.”Here an exemplary number 678 is shown; no limitation on a, “number” isimplied by this example. 1 e is a, “second encoding.” indicated by anarrow from the second exemplary number 678 to a, “second encoding” ofthe second number.

1 f is a result of the first encoding 1 c, which is shown marked as a,“first marking,” arrow 1 g, onto the first animal, Animal #1. Note thatelement 1 f in the figure is a human readable encoding of the exemplaryfirst number, 348, 1 b. Here, element 1 f is shown in a particular font,which may be appropriate for use both as a tail tattoo, and humanreadable, as one exemplary embodiment of a first encoding and a firstmarking.

1 h is a result of the second encoding 1 e, which is shown marked as a,“second marking,” arrow 1 i, onto the first animal, Animal #1. Element 1h is here, a vine code with a spine, one non-limiting embodiment of asecond, machine-readable encoding.

The first and second numbers, 1 b and 1 d, as encoded by encodings 1 cand 1 e, are also marked on a second animal, Animal #2, as shown byarrows 1 n. Thus, Animal #1 and Animal #1 have the same pair ofmarkings. They may be distinguished in a vivarium or study by“non-overlapping” time windows T1 and T1.

Limitation (j), “a first primary key associated with the first animal,”is shown by the exemplary, “first primary key,” 38745, by the statement1 j in the Figure, “38745 Primary Key for Animal #1.”

Limitation (k), the association between the first number (here, 348),the second number (here, 678), and the first time window (here, timelineT1) with the first primary key (here, 38745), is shown as arrow 1 k. Thelimitation, “not associated with any other primary key,” is shown by thestatement 1 l, “Each animal has a unique Primary Key.”

1 m shows an exemplary, “second primary key,” here, 99471.

Limitation (o), the association between the first number (here, 348),the second number (here, 678), and the second time window (here,timeline T2) with the second primary key (here, 99471), is shown asarrow 1 o.

Limitation (p), the unique association between the first number (here,348), the second number (here, 678), and the second time window (here,timeline T2) with the second primary key (here, 99471), is shown asstatement 1 p.

1 s, in the Figure, shows first and second time windows T1 and T2, “havenon-overlapping lifetimes.”

1 t in the Figure, shows that exemplary animals Animal #1 and Animal #2in a, “first animal population” are in a vivarium, 1 a.

1 q, in the Figure, shows limitation (q), “the first number and secondnumber are distinct.” Note that 348 and 678 are non-limiting exemplarynumbers.

1 r, in the Figure, shows that the first and second encodings, 1 c and 1e respectively, are distinct, limitation (r).

Human-readable markings may also be machine-readable.

In most cases, there is nothing to prevent a person from reading amachine-readable marking.

The head 53 and the tail rollers may be operated manually or may beautomated. Many different configurations of manual and automated markingdevices are possible. For manual operation, fingers may replace therollers 55 and the head 53 may be a hand-held tattooing head. As shownschematically, such a machine is capable of marking both human-readableand machine-readable markings. FIG. 1 shows an exemplary result ofmarking a rodent tail.

Both control of the operation of the machine of FIG. 8 and theverification of correctly marked codes may be performed by the use of asingle video camera, not shown in this Figure. Such use of a singlecamera for both purposes is an embodiment.

An alternative embodiment to traditionally tattooing is to damage,abrade or puncture the skin on the rodent tail either before afterapplying ink. Such action may be caused by an automatically controleeneedle or knife, or a laser. In one embodiment the ink is appliedmanually, in bulk, either before or after damaging, abrading orpuncturing the skin in the pattern to be marked on the tail.

An alternative embodiment to traditionally tattooing is using an ink jetprinter print head to apply ink. The skin of the rodent tail may bedamaged, abraded or punctured prior to applying the ink via the printhead. One advantage of using an ink jet print head is the ability toeasily use colored ink. Such an embodiment is specifically claimed. Inone embodiment this color is used to identify a mouse within the scopeof one cage. The color may be part of one of the code portions describedherein, or may be an additional marking.

An embodiment comprises reading codes as described herein, includingdevices of reading and methods of reading. Embodiments include systemsthat use both reading and writing, which might be use, for example, as acomprehensive animal identification system in a vivarium.

Additional Embodiments

Embodiments of this invention explicitly include all combinations andsub-combinations of all features, elements and limitation of all claims.Embodiments of this invention explicitly include all combinations andsub-combinations of all features, elements, examples, embodiments,tables, values, ranges, and drawings in the specification and drawings.Embodiments of this invention explicitly include devices and systems toimplement any combination of all methods described in the claims,specification and drawings.

Embodiments specifically include all independent claim limitations inall combinations with all independent claims.

Embodiments are claimed wherein the word “comprises” is replaced withthe word, “consists,” in one or more places in a claim.

Definitions

Code—The term, “code” has three different meanings depending on context.(i) It may be a method, algorithm, set of rules, or a standard ofcreating a mark or marking from an input, such as number oralphanumerics. For this meaning the word or process, “encoding” may beused, instead. (i) It may refer to the mark or marking itself. (iii) Itmay refer to entire process that comprises the first method, (i), asonly a part of that process. For meanings (i) and (iii), one mayconsider that the encoding has an “input” and an “output.” Nearly allencodings have a reverse “decoding.” The input to an encoding may have awell-defined input symbol sets. The output of an encoding will have awell-defined output symbol set. An encoding may be the use of a font.

Combination—any combination of members of a set, including a null setand all members of a set, unless otherwise stated or obvious. Theelements of the combination may be ordered or unordered. The elementsmay have fixed positions, or may have variable positions, or may have nopositions.

Distance—The distance between two elements may be viewed generally as aHamming distance, although different embodiments may compute distancedifferently, including modifications to a traditional Hamming distance.See www.wikipedia.org for industry technical description of Hammingcodes. For embodiments herein, for numeric characters based on a“seven-segment” layout, each “hamming symbol” is one of the sevensegments. The Hamming space may then be viewed as a binary 7-dimensionalspace. For leaves in a vine code where each leaf has four possiblestates (e.g. length) the Hamming space is a binary space with 4dimensions. A distance for two specific single symbols in a symbol setgenerally sums the Hamming distance for all pairs of elements (wherethese elements are the “Hamming symbols”) of the two symbols. A distancefor a first group of symbols and a second group of symbols generallysums the Hamming distance for all respective pairs of symbols in the twogroups. However, minimums or maximum distance may be used for selection.Note it is important to distinguish “Hamming symbols” from symbolsmarked as outputs from codes, such as one full decimal digit or one fullleaf in a vine code. As a shortcut of referring to the Hamming distance(or other distance calculation) of output symbols from an encoding wemay refer only to the distance of two input symbols or input values.

Distinct—two or more elements are distinct if they are not the same, ornot effectively the same in the described context. For example, twonumbers are distinct if they are not the same number. Two or moreelements may be non-tangible or abstract elements, such as the set ofnumeric characters and the set of alphanumeric characters, or calculusand algebra. As another example, Code 39 is distinct from Code EAN 5.

Leaves—see definition for vine code. A null leaf is one that has nomarking in the location for that leaf.

Pathogen-free—means the population of microbes, including but notlimited to bacteria, viruses, prions and toxins, relevant to theexperiment, are sufficiently reduced to meet the needs of the study, orto not impact the health, performance or behavior of the target animalpopulation or of the workers.

Primary cage or home cage—the cage in which an animal spends more timethan any other cage. Of note, there is a related term of art: “homecage.” The definition of primary cage is, in some embodiments, the homecage. An aspect of home cage/primary cage deals with the fungibility ofthe actual cage itself. Each time a cage is changed, the physical cageis generally either disposed of or removed for washing, and replaced bya clean cage. The new physical cage is considered the same primary cage.A primary cage may sometimes be distinguished from a non-primary cage bythe purpose of the cage. For example, a home cage may be for living in,as compared to an experimental cage to which the animal is transferredthat is equipped or located for one or more particular experiments forthe applicable study.

Sealed enclosure—an enclosure sealed against pathogens that impact oralter study results, or alter the credibility or repeatability of studyresults, entering or leaving the enclosure.

Sensor—may or may not include the use of local or remote processors, andmay or may not include local or remote software executing on the localor remote processors. Sensors may or may not communicate over a network.Multiple sensors may or may not include common elements.

Spine—see definition for vine code.

Sterile—pathogen-free.

The primary cage is different from special purpose,behavioral-measurement, behavioral-detection, or behavioral-observationcages that are generally used for only a short time for the duration ofa particular test due to cost and mindset.

Unique—occurs only once in the context or set defined to contain theelement

Vine code—a code, generally machine-readable, generally not commonlyhuman-readable, comprising a series of line segments of varying lengths,or varying positions, or both. Typically the line segments are placedparallel to each other with a gap in between. An axis may be definedperpendicular to such parallel line segments. The line segments may haveone end aligned with the axis or may, in some cases, cross or not crossthe axis depending on the choice of the line segment. Data is encoded inin the vine code by the variations in line length or position. Each linesegment is called a leaf. The vine code may or may have starting orending line segments, or both. Such starting or ending line segments mayor may not encode data. Some leaves in some codes are missing.Generally, all line segments are equally spaced relative to the axis.The axis may or may not be printed or readable. A vine code may bemarked in visible ink or may be marked using some other readabletechnology, including infrared, ultraviolet or magnet material. A vinecode may be overlaid with another code such that they can be readindependently. For example, a vine code may be printed in infrared inkwhile a human-readable marking is printed overlaid in violet or blueink. Filters may then be used to select one code over the other forreading. A human eye would not normally be able to see the infrared orultraviolet ink.

Ideal, Ideally, Optimum and Preferred—Use of the words, “ideal,”“ideally,” “optimum,” “optimum,” “should” and “preferred,” when used inthe context of describing this invention, refer specifically a best modefor one or more embodiments for one or more applications of thisinvention. Such best modes are non-limiting, and may not be the bestmode for all embodiments, applications, or implementation technologies,as one trained in the art will appreciate.

May, Could, Option, Mode, Alternative and Feature—Use of the words,“may,” “could,” “can,” “option,” “optional,” “mode,” “alternative,”“typical,” “ideal,” and “feature,” when used in the context ofdescribing this invention, refer specifically to various embodiments ofthis invention. Described benefits refer only to those embodiments thatprovide that benefit. All descriptions herein are non-limiting, as onetrained in the art appreciates.

What is claimed is:
 1. A system of marking animals in a (a) vivariumusing an animal identification code comprising: (b) a first number; (c)wherein the first number is suitable to be encoded by a first encoding;(d) a second number; (e) wherein the second number is suitable to beencoded by a second encoding; (f) a first marking; (g) wherein the firstmarking is an output of the first number and the first encoding, andwherein the first marking is human-readable, and wherein the firstmarking is permanently marked on a first animal; (h) a second marking;(i) wherein the second marking is an output of the second number and thesecond encoding, and wherein the second marking is machine-readable, andwherein the second marking is marked on a first animal; (j) a firstprimary key associated with the first animal; (k) wherein a combinationof the first number, the second number, and a first time window isassociated with the first primary key and not associated with any otherprimary key; and wherein the first time window is associated with anexpected lifetime of the first animal; (l) wherein the first primary keyis associated uniquely with the first animal in a first animalpopulation; and wherein an each animal in the first animal population isassociated with an each respective primary key, and wherein at leastsome animals in the first animal population have non-overlappinglifetimes; (m) a second primary key; (n) wherein the first marking ispermanently marked on a second animal; and wherein the second marking ispermanently marked on the second animal; (o) wherein a combination ofthe first number, the second number, and a second time window areassociated with the second primary key and not associated with any otherprimary key; and wherein the second time window is associated with alifetime of the second animal; (p) wherein the second primary key isassociated uniquely with the second animal in the first animalpopulation; (q) wherein the first number and second number are distinct;(r) wherein the first encoding and the second encoding are distinct; (s)wherein the first and second time windows do not overlap; (t) whereinthe first animal population is in the vivarium.
 1. The system of markinganimals of claim 1 wherein: the first and second markings are tattoos.2. The system of marking animals of claim 1 wherein: the first andsecond markings are tattooed on a tail of the first animal and tattooedon a tail of the second animal.
 3. The system of marking animals ofclaim 1 wherein: the first and second animals are rodents.
 4. The systemof marking animals of claim 1 wherein: the first and second animals aremice or rats and the markings are tattooed on the tails of the animals.5. The system of marking animals of claim 1 wherein: no other markingsare affixed to either the first animal or the second animal.
 6. A methodof marking animals in a vivarium comprising the steps: creating aproposed, unique primary key for a first animal in a first population ofanimals in the vivarium; selecting a first time window responsive to anexpected life of the first animal; selecting a first number; selecting asecond number; verifying that a combination of the first number, thesecond number and the first time window is not associated with anyexisting primary key in an animal database; associating the combinationof the first number, the second number and the first time window withthe proposed, unique primary key for the first animal; adding theproposed, unique primary key to the animal database as a new primarykey; encoding the first number with a first encoding to output a firstmarking; encoding the second number with a second encoding to output asecond marking; marking the first animal with the first and secondmarkings; wherein the first number and the second number are distinct;wherein the first encoding and the second encoding are distinct.